Viash Hub

Description

No description provided.

Input arguments

Name	Type & Properties	Description
--input_r1	file required multiple	Forward reads in FASTQ format. Multiple files corresponding to different lanes can be provided which will be demultiplexed separately before joining the results for each individual well.
--input_r2	file required multiple	Reverse reads in FASTQ format. Multiple files corresponding to different lanes can be provided which will be demultiplexed separately before joining the results for each individual well.
--barcodesFasta	file required
--umi_length	integer	Length of the UMI sequences
--genomeDir	file required
--annotation	file required
--sample_id	string	Sample ID for the provided input files. If not provided, the value of --id will be used. Input files will allways be demultiplexed separately, but the FASTQs for wells with matching sample IDs will be concatenated before mapping.

Name

Type & Properties

--input_r1

file

required

multiple

--input_r2

file

required

multiple

--barcodesFasta

file

required

--umi_length

integer

--genomeDir

file

required

--annotation

file

required

--sample_id

string

Output arguments

Name	Type & Properties	Description
--fastq_output	file required multiple output	Directory containing output fastq files
--star_output	file required multiple output	Output from mapping with STAR
--nrReadsNrGenesPerChrom	file required output
--star_qc_metrics	file required output
--eset	file required output
--f_data	file required output
--p_data	file required output
--html_report	file required output
--run_params	file output

Name

Type & Properties

--fastq_output

file

required

multiple

output

--star_output

file

required

multiple

output

--nrReadsNrGenesPerChrom

file

required

output

--star_qc_metrics

file

required

output

--eset

file

required

output

--f_data

file

required

output

--p_data

file

required

output

--html_report

file

required

output

--run_params

file

output

Run this component

Run the following command to execute this component with Nextflow:

cat > params.yaml <<'EOM'  
umi_length: [ 10 ]  
fastq_output: "$id.$key.fastq_output._*"  
star_output: "$id.$key.star_output._*"  
nrReadsNrGenesPerChrom: "$id.$key.nrReadsNrGenesPerChrom"  
star_qc_metrics: "$id.$key.star_qc_metrics"  
eset: "$id.$key.eset"  
f_data: "$id.$key.f_data"  
p_data: "$id.$key.p_data"  
html_report: "$id.$key.html_report"  
run_params: "$id.$key.run_params"  
id: "run"  
publish_dir: "output/"  
EOM

nextflow run https://packages.viash-hub.com/vsh/htrnaseq.git \  
  -revision v0.11.0 \  
  -main-script target/nextflow/workflows/htrnaseq/main.nf \  
  -params-file params.yaml